I process lots of files via the command line, e.g. using my own shell or python scripts. Is there an easy way to add the files that I manipulate to the Unity "recent files" list so I can then easily access them via the Unity dash?

Your shell scripts can use dbus-send to work with the lower-level D-Bus API.

However, I can't give an example because I haven't yet used either. (I use Lubuntu normally and I only know about Zeitgeist because my brother asked me to figure out how to clear out the Recent list in the Unity Dock)